Not really I wouldn't mind at all if they dropped Aenema in favor of something else.

They didn't, they just missed it out.
I would mind if they dropped it personally. From experience of seeing them at a small venue, i thought it was their best song that night. At bigger venues it's not as good though. For me Aenema is the song that makes a Tool show the perfect Tool show. I hope they finnish with that every time i see them from now on.